The Sins of our Past
by Spacelesschief
Summary: This is a short story twist that covers what I believe went down on the Citadel in Mass Effect 3 and all of the events that followed. This will lead in to a new adventure with a recovering galaxy where Shepard is around.
1. Prologue

Mass Effect: The Sins of our Past

Prologue: The Life of Jason Shepard as we know it

The great Jason Shepard, hero to some and villain to others; he saved the galaxy a number of times from a great number of threats. However not all his actions have been viewed upon in a good light. Born as a spacer and living his entire life on ships, joining the Alliance at eighteen was a natural choice to follow in his parents footsteps. After this fate looked upon him for the first of many times and he became a war hero, holding the line against impossible odds. The tale of this great hero continues as we all know on a routine mission to Eden Prime. What could possibly go wrong? What followed was a great journey of chasing the rouge Spectre Saren and the Reaper Sovereign.

On this great journey many lives were saved and legacies were created. On the snowy world of Noveria, the Rachni Queen was set free to begin anew with lessons learned. On the planet Virmire Captain Kirrahe and his squad was saved to fight another day along with Ashley. However not all survived to see it through, Kaiden Alenko was killed in action on so that everyone else could escape. Plus he even managed to save the Feros colonists, Exo-Geni science team, and an Asari under the thrall of the bizarre and ancient creature known as the Thorian which he proceeded to destroy. On a bright note in his mission, Shepard thwarted a Batarian terrorist attack upon a human world via dropping an asteroid upon said planet. Saving Balek to preserve lives in the process, Balek went off to do who knows what and the colony lived to see another day. Lastly on Shepard's journey to save the galaxy, he sacrificed the Citadel Council in order to preserve the Alliance fleet to assault Sovereign. With Sovereign destroyed and humanity forming the basis for the new Council, Shepard was sent into the Terminus systems to wipe out the remaining Geth.

Unfortunately the Collectors got to Shepard and destroyed the Normandy SR-1, killing Shepard and large number of the crew. His last moments were spent with his love Liara as well as Joker and, the dying Normandy. The Collectors proceeded to kidnap human colonists across the Terminus systems for an unknown goal. Unbeknownst to the galaxy at large, yet suspected by Cerberus was the fact that the Collectors were actually controlled by the Reapers. Cerberus, looking to further a greater human agenda; wished to stop these abductions and resurrected Shepard to combat the Collectors and ultimately stop the Reapers from invading. So two years after his death, Shepard was awoken for the first time to go on his next journey across the galaxy.

The next installment of Shepard brought the renewed Spectre deep into the Terminus systems to fight the Collector menace far from Council space. Gathering an amazing and large team mixed of old friends and new, Shepard gathered them up, settled their differences and gained all of their loyalty in preparation for what was sure to be a suicide mission. With all of their help, the mission turned out to be anything but a suicide mission as the collectors were defeated, the base preserved and no more lives were lost. Once more the Reapers were thwarted and forced to begin the long trek through dark space to get into the Milky Way galaxy.

After the suicide mission, Shepard began a series of missions for both Cerberus and old friends alike. Beginning with a trip to the planet Aite to determine what happened to the Cerberus project Overlord. What he found was more than anyone bargained for as all but two had been killed in the project, the leader and his autistic brother who was in fact the rogue VI that had killed everyone. By the end, Shepard had had enough and decided to free David Archer from his prison and send him to Grissom Academy.

Next on his mission list was to assist his love, Liara T'Soni in taking down the Shadow Broker and to free her friend. In a crazy twist and turn adventure, the pair found themselves at the Shadow Brokers ship and discovered that the Broker is in fact a Yahg, a race that was forced to stay on their planet for being too barbaric after killing the visiting Council races. After a difficult fight, the Broker was killed and Liara took his place in order to better combat the Reapers and help find any way of stopping them.

Several months before the Reapers were to land, Admiral Hackett asked a favor of Commander Shepard to go check on an alliance project that was in a Batarian system and had gone silent. Shepard traveled there to rescue Doctor Kenson from the Batarians, after rescuing Doctor Kenson he then learned that the Reapers arrival was just days away. Going to confirm the artifact and the time until arrival, he was betrayed by an indoctrinated Kenson and the rest of the science team that is also indoctrinated. After being knocked out and waking up with just hours to spare, Shepard kills Kenson and most of the science team while activating "the project" thereby destroying the relay. Shepard escaped just in time, living to fight again, meanwhile over three hundred thousand Batarians died to delay the return of the reapers.

Finally, the day came and the reapers arrived in the known galaxy. They blasted through the Batarians straight out of the gate, then hitting humans shortly after. Before long the entire galaxy was at war with the reapers. Shepard had been ordered to leave Earth behind during the attack to go rally support, and with knowledge from the Prothean archives on Mars Shepard was able to give the galaxy a fighting chance.

This chance was hard won, curing the Krogan Genophage with the assistance of Mordin Solus, Eve, and Wrex so that Palaven could receive the Krogan support it needed to relieve the pressure upon the planet. Retaking Omega for Aria to unite all the pirates under her leadership so as to have more ships and guns blowing up reapers was rather difficult to achieve. Unifying the Quarians and Geth, thereby ending the Quarian exile from their home world, all it cost was the loss of legion and far too many Quarians. Continuing on, those of the past, old and ancient were awoken to assist against the reapers. The Prothean Javik and the apex species, those known as Leviathan and his fellow survivors, all came together in an unlikely alliance with the other races of the galaxy to take on the Reapers at one final fight at Earth.

Once more unto the breach the heroes went, one final stand, one last fight, at Earth. This was to be the battle of battles that managed to bring Shepard and Anderson to the Citadel to end the cycle. Confronting the Illusive Man and the child, Shepard made the decision to change the fate of the galaxy. He chose to destroy the Reapers, and according to the child, all synthetics would be destroyed.

Those lost along the way were Legion, who sacrificed himself to unify the Geth with the Quarians and to provide the ultimate upgrade to the Geth.

Mordin Solus who died to cure the Genophage, a horrible mistake he now fixed so that the Krogan had the opportunity to rise again.

Thane Krios lost his life protecting the Salarian Councilor, a good fight, if albeit against a lesser foe.

Lastly Admiral Anderson died at the hands of Shepard under the control of the Illusive Man.

All of these people and potentially thousands, millions or even billions more died because of the invasion and Shepard's choice to destroy synthetics. But what really happened after Shepard fired the Crucible? What happened to his love Liara and the crew of the Normandy, or the rest of the species? Was the child telling the truth? Or was he trying to influence Shepard into making a different decision? This is the story of what happened to the galaxy after Shepard changed the course of history forever.


	2. Chapter 1

So for anyone who may have difficulty following what goes on in this story. I chose to expand upon the indoctrination theory of old, mess with it a bit and come out with a whole new story. A couple of things beyond that in mass effect 3 struck me as odd anyways, like where Shepard went to open the Citadel arms. We already know from mass effect 1 that the control center is in the Council chambers at the top of the tower, why would they go anywhere but there? Anyways here is the first installment, enjoy.

The Sins of our Past

Chapter One

"Where… where am I?" What… OW! Everything hurts like crazy. Wow ok, think Jason, what did I last do? Uh, Reapers, war, Crucible, Crucible! I shot at the Crucible! I ran down the hill, got hit by Harbinger, ran into the beam, found the Illusive man and Anderson. Oh Anderson, damn… Well if I lay here a bit, maybe my eyes will adjust. Maybe get a decent idea of where I am.

As Shepard lay there for a few seconds, shapes began to take form, the darkness faded and much to his surprise the pain started to fade all over his body.

This looks familiar. Sort of like the Citadel, but what is that insistent buzzing? What if… my armor! It wasn't damaged! "Ok what the hell happened? Shouldn't I be dead or dying?"

"Who else made it to the Citadel? Any sign of Shepard?" a voice said in placement of the buzzing in Shepard's ear.

"Not that I can see Admiral. Shepard went up the beam, but we aren't entirely sure what happened. One second he was running down the hill, the next he stumbled and slowed to a walk. In all the confusion everyone just kept running. I caught up to Shepard just as he was going up, but when I arrived no one was here." This responding voice sounded a lot like Anderson, but that couldn't be, Anderson had died. Right?

"All right Admiral, proceed to the Crucible, find the control panel and open the arms. We need to dock the Crucible with the Citadel. For whatever reason Harbinger has stopped moving, reports say he is just standing there. I have no idea why but this break is what we need to get the crucible docked." The first voice said again, which strangely sounded a lot like Admiral Hackett.

With almost all the pain gone, including the wicked headache that was fading away. Shepard thought he felt the lingering presence of a powerful like entity in his head fading away. When he then heard a familiar voice say in his head "releasing control."

"Harbinger?" Shepard thought out loud. Was I just, controlled by Harbinger? Well whatever it was, it can wait. "This is Shepard, can anyone hear me? I'm on the Citadel, something happened and it knocked me out cold but I'm up. Anderson can you read me, its Shepard, I made it up?"

"Shepard!" Where are you?" replied Admiral Anderson.

Taking a quick stock of his surroundings, Shepard took in as much as he could noticing that it appeared similar to his strange dream like sequence. But was more like the Citadel he recognized than the strange mesh of architecture that the dream had.

"There are bodies everywhere of all species, all dead I think. I see a door in the distance; I will head to it and see where it goes. Although I'm not sure where I am, I don't recognize this area of the Citadel."

"Commander, this is just a guess but I think that this may be a hidden area no one was able to find where the keepers went. In the past no one knew where the keepers came from, just that they showed up. We could all be in some sort of processing rooms converted by the keepers to receive bodies." Replied Major Coats.

"I agree Major, it's the best guess we have, but the only location I know of to open the arms is in the Council chambers. If we find that, we can open the arms. Shepard, what is your progress?"

In the time during the conversation Shepard had taken stock of his gear and made it to the door, opening it and finding himself surrounded by somewhat familiar architecture.

"I walked through the door, and I think I'm somewhere on the Presidium. That or really close to it. More bodies, a lot of them, the keepers have been busy."

"All right everyone, in total there are about twenty of us up here. Hopefully we all ended up on the Presidium level. Make your way to the Citadel tower. But make sure you meet up with at least one other person before moving on. Who knows what the hell is waiting for us up here."

Everyone understood and checked out, moving on to find the Council chambers and hopefully one another in time to make a difference and destroy the Reapers. Shepard himself pushed on through the hidden halls.

"Admiral Hackett sir, Harbinger is moving again he is following the other Reapers back up here to the fight."

"There is nothing we can do about it right now." Activating the fleet communication again Admiral Hackett gave new orders. "Everyone, people have made it up into the Citadel. Now it is up to us to hold out as long as we can. Protect the Crucible at all costs. Geth and Quarian fleets, try to draw the Reaper forces away from the Crucible."

In response several confirmations came over the fleet communication and the fleets did the best they could to follow the orders while fighting the much more powerful Reapers. As the Geth and Quarian fleets pulled away, some of the Reapers turned and followed them. Unfortunately it was much fewer than the Admiral had hoped that would.

The good news is that with the variety of strategy and technology, the Geth and Quarians shouldn't fair too badly against so few Reapers. Added is that they aren't restricted to guarding the Crucible so they can let loose. However, it won't make a big enough dent to give us more time. The Admiral thought to himself. This fight could be going much worse though. With the sheer number of ships that Shepard had managed to bring to the fight, the Reapers were actually having a bit of a challenge. The question was though, is it enough?

Noting that the Normandy had made it back up to the fight, he came up with an idea that might help. "Normandy, now that you are back up here. I am going to send some thankix cannon equipped frigates your way. Your orders are to harass Harbinger, keep him from getting close."

Responding over the communication channel was EDI rather than Joker. "We understand we will attempt to keep Harbinger from approaching the Crucible."

With that Hackett took a step back to look at the larger conflict again. Strategy was beyond difficult against the Reapers, especially since traditional tactics just seemed so pointless. Flanking or drawing enemy away just didn't have the intended effect. Lining the ships up like the British troops of old and firing massive salvos seemed to get the job done in taking down Reapers. But it was a matter of sacrifice; choose which ships to die to take down a Reaper here, so that at least one was taken out. However with so many ships dying at once for a single Reaper was not going to work. As a matter of fact, the best strategy was an accident. With all the ships and Reapers intertwined in space, some Reaper shots missed or cut through so effectively that they would hit a Reaper on the other side.

In space, the battle continued to rage. Ships working together to take down single targets in the hope it brought about the desired effect. Every second, a Reaper or more often an allied ship blew up. The only fight going well for the species of the galaxy was the snub-fighter squadrons. Elsewhere the Geth-Quarian Fleet was going quite successfully, with the Quarian live ships keeping distance with a Geth Dreadnaught firing the heaviest weaponry they had. Almost taking out an entire Reaper each time all the ships fired. The entirety of the battle however was utter chaos.

Well, well would you look at this. Thought Shepard as he ran through the hidden halls of the Citadel that Major Coats suspected the keepers used to get around and came to a halt as a door opened into the location he least thought he would walk into. The personal room of Sha'ira, the asari consort. "While I could use her help with that strange dream, I doubt she is even alive nor do I have the time to talk to someone about a dream." Continuing on opening the door to leave, through the door was a make shift barricade with several dead husks, but no other bodies. The walls were riddled with bullets, clearly the position was being defended but as to where the defenders had vanished to, there wasn't a trace.

Moving on through the consorts chambers and exiting into the main presidium walk area; Shepard was able to see the Tower in the distance. "This is Shepard, I'm in the presidium outside the consorts chambers, and I can see the tower. Is anyone else nearby?"

"Shepard, this is Lieutenant Elizabeth Boone, I'm across the presidium from you, a bit closer to the tower. I am with three other Marines; there is a bridge near us. If you can get to it, take it across and we will wait for you and meet with you on the other side.

"Understood, heading there now." Shepard replied

Finding the bridge was easy, almost too easy. Why hadn't the Reapers put any forces up here? In fact where were the bodies? After exiting the Consorts chamber and entering into the general presidium, there had not been a single body, husk or otherwise. Shepard found this very odd. Very different from how his dream had looked or whatever it was. Where in the dream there were a lot of bodies in the first room with a keeper. But he tried not to think about it too hard as he pushed on to this Lieutenant Boone and her squad. All that mattered was opening the Citadel; the dream could wait until the mission was over.

All around Shepard, despite the lack of bodies and enemies, the entire presidium looked shot to hell. Bullet holes all over the place, explosive residue, blood splatters. Everything one would expect from a big battle. Nearing the bridge, Shepard kept his attention ahead. Rounding a corner, Shepard found the one thing he did not want to see. The first body after the ones in the Consorts chamber, a Cerberus Trooper was dead on the ground. Although what exactly caused his death wasn't exactly clear.

Before Shepard could report his discovery, over the radio came the panicked voice of Lieutenant Boone.

"This is Lieutenant Boone! We are under attack by Cerberus." Gunfire could be heard in the background, a lot of fire. They came out of nowhere! One man down! We need backup!"

"Shepard, double time it. Get there now!" Anderson commanded over the comm.

"Yes sir!" Shepard replied as he started running to the bridge mentioned earlier. Explosions and gun fire could be heard across the presidium lake. But in the distance he noticed a squad of Cerberus soldiers approaching the Citadel tower. If they made it up there first… well who knows what they could do. But if they wanted to control the reapers they would need the Crucible attached just as much as anyone else. Assuming of course that Cerberus wasn't being controlled by the Reapers, and the Illusive Man wanted to try and control them. With the clock ticking, Shepard made the choice to save the squad and hope luck was with him.

"Anderson! I'm heading over the bridge to the squad right now, but there is a group of Cerberus soldiers nearing the tower. We need to head them off, if we don't…" Shepard left the rest unsaid, for everyone knew what the potential consequence would be if Cerberus got there first.

"We'll just have to let them go; we can catch up and deal with them later."

Running full tilt over the bridge, Shepard pulled out his shotgun and biotic charged at a Cerberus soldier who was getting a little to close the stranded marines than was comfortable. Upon landing the trooper went flying, hitting the wall with a very obvious snap sound at the breaking of his neck or back. Blasting to more nearby soldiers with his M-11 Wraith shotgun, Shepard took stock of the situation and then threw a shockwave at the Cerberus troopers in cover. With the shockwave traveling towards them, Shepard took cover. Meanwhile Boone and the other surviving marine popped up during the distraction provided by Shepard and poured ammo and tech abilities at the Troopers. With their lines broken and only a few near Shepard and the marines to cause trouble, it was short work to wrap up the few left. Unfortunately the distraction of fighting the Troopers was enough for several more to skirt the battle and make a straight shot to the tower.

"Marines! Status? You guys doing all right?" Shepard asked.

"Yes sir, I'm not missing any body parts anyways."

"Same here sir, a little banged up but I'll live."

"All right then, let's move out. No time to stand around; double time it to the tower. We can meet up with anyone else at the base of the tower." Shepard ordered while scanning the Presidium around to see if there were any more Cerberus troopers or more hopefully, some marines nearby. Curiously there was no one in sight nor was there any sound. Eerily quiet.

While running to the tower, Shepard activated his comm. "Anderson, we are almost at the tower now, two marine survivors. No one else was in sight including Cerberus."

"Well if we are lucky that's the last of Cerberus we will see, not holding my breath though. Major Coats and I met up with another Marine but I think everyone else is dead. No is reporting in." Over the comm Shepard could hear Anderson sigh. "We are on the other side of the Presidium by the markets; we will pass right by the relay monument. ETA is two minutes to the tower."

Meanwhile Shepard and the Marines had made it to the tower elevator and had secured the position. Without knowing how many troops were up the tower, there was no way to know how big of a fight was in store for them. So they had to wait for Anderson for the extra numbers. Being this close to the end, they couldn't afford the risk to lose it all right now. True to his word, Anderson appeared crossing the bridge in front of the tower near the relay monument. Much to everyone's surprise, the wait for Anderson and the elevator as it made its way down was strangely uneventful.

"Shepard, it's good to see you alive after all that hell we went through to get here. How are you holding up?" asked Anderson once he got to the tower, with a worried look on his face as if he knew something had happened to Shepard that he didn't remember.

Responding first with a strong handshake, Shepard replied "I'm doing good, still a little fuzzy on details of getting to the Citadel but I'm one hundred percent ready to go. How about you Anderson? Keeping up with these young marines?"

"Not bad, feels like years since I just sat down, and I don't even have the luxury of doing that right now." Chuckling to himself a bit Anderson continued, "Heck, it may just be a few more years before I even get to sit down again."

Suddenly remembering that Anderson had said those almost those exact words just before he died in his dream, he made to comment on it. But the elevator arrived before he could say anything. With the door open and it empty, they all clambered in, barely fitting the six of them inside and started the elevator to the top.

"I'm surprised this thing is managing to hold all of our weight, we must weight a ton." Lieutenant Boone mentioned.

"Shepard, it looked like you were about to say something, something on your mind?" asked Major Coats

Suddenly forced and unable to speak of the dream, Shepard defaulted to something else to say. "Oh nothing really, just that the last time I was in this elevator loaded up like this; I was fighting an army of Geth trying to battle my way to Saren and Sovereign back when they first attacked the Citadel. The elevator was stopped in the tracks and we had to fight outside the tower the rest of the way to the top."

Anderson seeing the hesitation got even more worried when a random Marine said "Dang sir, I hope Cerberus didn't think that far ahead…. when Shepard suddenly blacked out as if the elevator had been stopped.

In Shepard's mind he faintly heard Harbinger say, "Assuming Control." Before he lost consciousness and fell to the ground.


End file.
